[maker-devel] unexpected alternate splicing

[Carson Holt]

Are you using gff3 files as input? If so, could you send those to me?  They are probably coming from thise.

--carson


Sent from my iPhone

> On Apr 29, 2014, at 2:21 AM, Malcolm Hinsley <mhinsley at ebi.ac.uk> wrote:
> 
> Hi
> 
> We've just reinstalled maker 2.31 using mpich3 (3.1) and are delighted that file locking and other issues have been resolved. (I'm running maker across several nodes on the compute farm). The maker code is identical: I took the previous tar.gz archive and made a clean build.
> 
> Using a copy of a previous configuration to test, the only differences I can see is that the location of some files has changed (the working directory is on a different file system) and that I'm using a bigger (unfiltered) repeat library.
> 
> The previous maker run produced  17393 genes and 17393 mRNAs, and this new version gives 15927 genes and 21328  mRNA.
> 
> I have alt_splice=0:
> 
> $ grep splice ../maker_opts.ctl
> alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no
> 
> 
> Any idea why I'm getting multiple mRNAs per gene?
> 
> -- 
> malcolm hinsley | EnsEMBL Genomes | +44 (0)1223 49 4669
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
> United Kingdom
> 
> 
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